The Whitehall department that sets whistleblowing policy has been identified as one of the worst for encouraging staff to come forward with suspicions of wrongdoing, according to an official assessment.

The Cabinet Office has offered poor access to independent advice and failed to offer an alternative to line management if staff wish to report matters of public interest at work, the National Audit Office has found.

The department's failings have been matched by the Treasury, which has also been criticised as "poor" under two of eight categories measured by auditors. George Osborne's department was found to have failed to support whistleblowers because of poor confidentiality and for access to independent advice.

The NAO reviewed 39 whistleblowing policies across government against eight different criteria. They found that the policies "sometimes failed to outline suitable alternatives to line managers when making a disclosure or explain when the confidentiality of a whistleblower may be compromised."

Cathy James, chief executive of the whistleblowing charity Public Concern at Work, said the results of the NAO's survey were troubling. "It is clearly good news that this work is being undertaken by the government's own watchdog on this key issue, but troubling that the department that sets government policy on whistleblowing [the Cabinet Office] is bottom of the table.

"A similar theme emerged when we looked at Whitehall whistleblowing policies in 2007 – back then the Cabinet Office again came bottom of the league," she said.

A spokeswoman for the Cabinet Office said that the department scored less than satisfactory on two elements of the survey. "All government departments have a whistleblowing policy, recognised by the NAO as generally of good quality. We want to ensure consistency across departments and will continue to work with the NAO to do so," she said.